[gmx-users] Does a logical pressure (1 Bar) can be reached in REMD?

[Justin Lemkul]

On 5/19/18 8:45 AM, Soham Sarkar wrote:
> Thanks for reply.. but what is the actual pressure of the system? You
> mentioned it as the instantaneous pressure

Instantaneous simply refers to the value at any given time point; these 
will fluctuate wildly, particularly for a tiny system like yours, and 
the instantaneous values are meaningless.

The average pressure (and its distribution) is more meaningful. Compute 
that with gmx energy.

-Justin

> On Sat, 19 May 2018, 6:03 pm Mark Abraham, <mark.j.abraham at gmail.com> wrote:
>
>> Hi,
>>
>> This is normal for instantaneous measurements of pressure. See
>> http://www.gromacs.org/Documentation/Terminology/Pressure
>>
>> Mark
>>
>> On Sat, May 19, 2018, 13:04 Soham Sarkar <soham9038 at gmail.com> wrote:
>>
>>>   Dear All,
>>> I have a small system including a 4 residue peptide. I have chosen 8
>>> temperature windows for doing REMD simulation of this system. After the
>>> temperature convergence of the 8 systems in the 1st stage of
>> equillibration
>>> run, the obtained pressure are quite absurd, which is not change that
>> much
>>> after the 2nd stage of production run. I want to know whether this type
>> of
>>> pressure range is ok for a system or not? Should I carry out analysis in
>>> this pressure range? As in normal md simulation there is a pressure
>>> convergence step which takes the system to the desired pressure. This
>> type
>>> of step is not there in the REMD simulation.
>>> The pressure and temperature of this system after 1st stage of
>>> equillibration of 10ns are as follows
>>> Temperature(K) Pressure(Bar)
>>> 350.112              -28.4761
>>> 369.218             262.054
>>> 389.201              592.84
>>> 410.074             946.021
>>> 429.12               1273.92
>>> 448.873              1628.61
>>> 469.438              2005.04
>>> 490.272              2392.50
>>>
>>>
>>> --
>>> SOHAM SARKAR
>>> Junior Research Fellow
>>> Department of Chemistry
>>> INDIAN INSTITUTE OF TECHNOLOGY BOMBAY
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================